ITunes shows 2,700 photos on my iPhone, but there's only 161 on the phone.

My iPhone's disc space is suddenly full. iTunes shows I have 7gb of photos (2,700)on my iPhone when I connect it, but my phone really only has 161.
I recently updated to iOS 4.0.1 on iPhone 3GS and iTunes 9.2.0.61 on Windows Vista. I was previously using iOS 3.1.3 and iTunes 9.0.xxx (not sure of which 9.0 version) and I had been using an App called Goodreader. I would transfer my files via USB with an .exe file called GoodreaderUSB to my iPhone. Now I can't since iTunes has been cracking down on that, and Goodreader uses iTunes to USB transfer with their new version and iTunes 9.2.xxx. I have a feeling my old USB transfers are all still in my phone, just unaccessible but iTunes is showing them as photos as far as disc space goes. This could be completely unrelated to Goodreader, but I have a strong suspicion it's the problem.
I've attempted multiple backups and syncs and I'm only syncing 84 photos (part of the 161 on my phone).
I also just realized it's showing 5.8gb of apps, when I did the math quick and only have 2gb of apps.
My iPhone also shows that I have used this much disc space when I run the app "System Activity Monitor."
Anyone know how to resolve this problem?
Message was edited by: skaguy58

GoodReaderUSB originally worked by transferring files to a special location on a user’s iPhone, which iPhone’s GoodReader app was able to access. However, accessing this location was a violation of Apple’s iPhone SDK Agreement, because the app had to access files outside its own private storage space, which is forbidden by Apple.
Because of this, your only choice to fix this. at this point, may be to restore your phone as a "new" device in itunes and NOT from backup. Follow this by syncing your content back to your phone. Unfortunately, ALL saved data on your phone will be lost.

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